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\name{ceScan-methods}
\docType{methods}
\alias{ceScan}
\alias{ceScan,Axt-method}
\alias{ceScan,CNE-method}
\title{ceScan function}
\description{
This is the main function for conserved noncoding elements (CNEs)
identification.
}
\usage{
ceScan(x, tFilter=NULL, qFilter=NULL,
tSizes=NULL, qSizes=NULL, window=50L, identity=50L)
}
\arguments{
\item{x}{
\code{CNE} object, or \code{Axt} object,
or \code{character}(n) object of Axt filenames.
}
\item{tFilter,qFilter}{
\code{GRanges} object or NULL: regions to filter out for
target and query assembly.
}
\item{tSizes,qSizes}{
\code{Seqinfo} object or \code{integer}(n) or \code{NULL}:
it contains the \code{seqnames} and
\code{seqlengths} for target and query genome.
When it's \code{NULL}, this \sQuote{seqinfo} must exist in \sQuote{x}.
}
\item{window}{
\code{integer}(n): the window size of scanning CNEs.
By default, it is 50L.
}
\item{identity}{
\code{integer}(n): the minimal identity score over the scanning window.
By default, it is 50L.
}
}
\details{
ceScan scan the axts alignments and identify the CNEs.
ceScan can accept axts in \code{Axt} object and regions to
filter out as \code{GRanges} objects,
or directly the \sQuote{axt} files and \sQuote{bed} files.
The details of the algorithm are described in the vignette.
}
\value{
A \code{list} of \code{GRangePairs} or \code{CNE} object is returned.
Each element of the list corresponds to one user-specified threshold for identifying CNEs.
}
\author{
Ge Tan
}
\examples{
library(BSgenome.Drerio.UCSC.danRer10)
library(BSgenome.Hsapiens.UCSC.hg38)
axtFnHg38DanRer10 <- file.path(system.file("extdata", package="CNEr"),
"hg38.danRer10.net.axt")
axtHg38DanRer10 <- readAxt(axtFnHg38DanRer10)
axtFnDanRer10Hg38 <- file.path(system.file("extdata", package="CNEr"),
"danRer10.hg38.net.axt")
axtDanRer10Hg38 <- readAxt(axtFnDanRer10Hg38)
bedHg38Fn <- file.path(system.file("extdata", package="CNEr"),
"filter_regions.hg38.bed")
bedHg38 <- readBed(bedHg38Fn)
bedDanRer10Fn <- file.path(system.file("extdata", package="CNEr"),
"filter_regions.danRer10.bed")
bedDanRer10 <- readBed(bedDanRer10Fn)
qSizesHg38 <- seqinfo(BSgenome.Hsapiens.UCSC.hg38)
qSizesDanRer10 <- seqinfo(BSgenome.Drerio.UCSC.danRer10)
## Axt object
windows <- c(50L, 50L, 50L)
identities <- c(45L, 48L, 49L)
CNEHg38DanRer10 <- ceScan(x=axtHg38DanRer10, tFilter=bedHg38,
qFilter=bedDanRer10,
tSizes=qSizesHg38, qSizes=qSizesDanRer10,
window=windows, identity=identities)
CNEDanRer10Hg38 <- ceScan(x=axtDanRer10Hg38, tFilter=bedDanRer10,
qFilter=bedHg38,
tSizes=qSizesDanRer10, qSizes=qSizesHg38,
window=windows, identity=identities)
## CNE object
cneDanRer10Hg38 <- CNE(
assembly1Fn=file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit"),
assembly2Fn=file.path(system.file("extdata",
package="BSgenome.Hsapiens.UCSC.hg38"),
"single_sequences.2bit"),
axt12Fn=axtFnDanRer10Hg38, axt21Fn=axtFnHg38DanRer10,
cutoffs1=8L, cutoffs2=4L)
## Here danRer10Filter is tFilter since danRer10 is assembly1
cneListDanRer10Hg38 <- ceScan(x=cneDanRer10Hg38, tFilter=bedDanRer10,
qFilter=bedHg38,
window=windows, identity=identities)
}
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